Are you sure it was related to the pollution/run off? Or is that just a guess?
It could possibly and simply be the fact you swam every day. A few years ago I bought my first house with a pool and have had a pool since. I swam every day for a couple years (~8 months/year), then this year I'm having a ton of swimmer's ear & sinusitis issues. My pool water is about as clean as it gets for outdoor swimming. And for me at least has been more correlated with frequency of contact with water than anything else. If my ears or sinuses act up, I take a week off from the pool and it gets better.
I cannot be 100% sure - see bio - but I am pretty sure.
All Key West waters are shitty water according to easily searchable stats, but rain runoff makes it much worse. [0]
To get to your point though, I had always hated chlorinated water even more. It will absolutely destroy your mucous membrane even if it is "clean." This destroys your first line of defense and can lead to all kinds of sensitivity after you leave the water. I believe that's the off-label benefit of those nose clips.
It could possibly and simply be the fact you swam every day. A few years ago I bought my first house with a pool and have had a pool since. I swam every day for a couple years (~8 months/year), then this year I'm having a ton of swimmer's ear & sinusitis issues. My pool water is about as clean as it gets for outdoor swimming. And for me at least has been more correlated with frequency of contact with water than anything else. If my ears or sinuses act up, I take a week off from the pool and it gets better.